TG-Gates_DifferentialExpression

Title: “Differential Expression Identification”

Purpose: “ASPIS omics Steatosis case study”

Input.data: “NormData_TG_Gates_Hum_invitro_ENS.txt”

Author: “Marcha Verheijen (ONTOX)”

Date: ‘2024-01-11’

Applied tools:

The R-ODAF pipeline (Omics Data Analysis Framework for Regulatory Application)

for Microarray technology was used. (Publication: “R-ODAF: Omics data analysis framework for regulatory application”, 2022, Regulatory Toxicology and Pharmacology.) This pipeline can be found at https://github.com/R-ODAF/Main and was based on:

ArrayAnalysis - affyAnalysisStat

Overview of samples and groups

Overview of array names and array groups
Array	Name	CompoundClass	Group	Group_Dose	SteatosisPotential	Group_Time	CompoundName	DoseGroup	Treatment	TimeDose	TimeDose_low	TimeDose_middle	TimeDose_high	TimeDose2	TimeDose_middlehigh	DoseValue	DoseUnit	Time	TimeUnit
003016027024.CEL	TG_hum_vit_Ami_ctl_2h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_2h	amiodarone_Control	Control	none	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	NA		2	hour
003016027025.CEL	TG_hum_vit_Ami_ctl_2h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_2h	amiodarone_Control	Control	none	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	NA		2	hour
003016028006.CEL	TG_hum_vit_Ami_ctl_8h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	amiodarone_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016028007.CEL	TG_hum_vit_Ami_ctl_8h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	amiodarone_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016028014.CEL	TG_hum_vit_Ami_ctl_24h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	amiodarone_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016028015.CEL	TG_hum_vit_Ami_ctl_24h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	amiodarone_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016027026.CEL	TG_hum_vit_Ami_280nm_2h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_2h	amiodarone_Low	Low	amiodarone	Steatotic_2h_Low	Steatotic_2h_Low			Steatotic_2h_Low		0.28	micromolar	2	hour
003016028001.CEL	TG_hum_vit_Ami_280nm_2h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_2h	amiodarone_Low	Low	amiodarone	Steatotic_2h_Low	Steatotic_2h_Low			Steatotic_2h_Low		0.28	micromolar	2	hour
003016028008.CEL	TG_hum_vit_Ami_280nm_8h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_8h	amiodarone_Low	Low	amiodarone	Steatotic_8h_Low	Steatotic_8h_Low			Steatotic_8h_Low		0.28	micromolar	8	hour
003016028009.CEL	TG_hum_vit_Ami_280nm_8h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_8h	amiodarone_Low	Low	amiodarone	Steatotic_8h_Low	Steatotic_8h_Low			Steatotic_8h_Low		0.28	micromolar	8	hour
003016028016.CEL	TG_hum_vit_Ami_280nm_24h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_24h	amiodarone_Low	Low	amiodarone	Steatotic_24h_Low	Steatotic_24h_Low			Steatotic_24h_Low		0.28	micromolar	24	hour
003016028017.CEL	TG_hum_vit_Ami_280nm_24h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_24h	amiodarone_Low	Low	amiodarone	Steatotic_24h_Low	Steatotic_24h_Low			Steatotic_24h_Low		0.28	micromolar	24	hour
003016028002.CEL	TG_hum_vit_Ami_1400nm_2h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_2h	amiodarone_Middle	Middle	amiodarone	Steatotic_2h_Middle		Steatotic_2h_Middle		Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	1.40	micromolar	2	hour
003016028003.CEL	TG_hum_vit_Ami_1400nm_2h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_2h	amiodarone_Middle	Middle	amiodarone	Steatotic_2h_Middle		Steatotic_2h_Middle		Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	1.40	micromolar	2	hour
003016028010.CEL	TG_hum_vit_Ami_1400nm_8h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	amiodarone_Middle	Middle	amiodarone	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	1.40	micromolar	8	hour
003016028011.CEL	TG_hum_vit_Ami_1400nm_8h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	amiodarone_Middle	Middle	amiodarone	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	1.40	micromolar	8	hour
003016028018.CEL	TG_hum_vit_Ami_1400nm_24h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	amiodarone_Middle	Middle	amiodarone	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	1.40	micromolar	24	hour
003016028019.CEL	TG_hum_vit_Ami_1400nm_24h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	amiodarone_Middle	Middle	amiodarone	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	1.40	micromolar	24	hour
003016028004.CEL	TG_hum_vit_Ami_7um_2h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_2h	amiodarone_High	High	amiodarone	Steatotic_2h_High			Steatotic_2h_High	Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	7.00	micromolar	2	hour
003016028005.CEL	TG_hum_vit_Ami_7um_2h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_2h	amiodarone_High	High	amiodarone	Steatotic_2h_High			Steatotic_2h_High	Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	7.00	micromolar	2	hour
003016028012.CEL	TG_hum_vit_Ami_7um_8h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	amiodarone_High	High	amiodarone	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	7.00	micromolar	8	hour
003016028013.CEL	TG_hum_vit_Ami_7um_8h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	amiodarone_High	High	amiodarone	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	7.00	micromolar	8	hour
003016028020.CEL	TG_hum_vit_Ami_7um_24h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	amiodarone_High	High	amiodarone	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	7.00	micromolar	24	hour
003016028021.CEL	TG_hum_vit_Ami_7um_24h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	amiodarone_High	High	amiodarone	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	7.00	micromolar	24	hour
003016018004.CEL	TG_hum_vit_Ctc_ctl_2h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_2h	carbon tetrachloride_Control	Control	none	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	NA		2	hour
003016018005.CEL	TG_hum_vit_Ctc_ctl_2h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_2h	carbon tetrachloride_Control	Control	none	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	NA		2	hour
003016018012.CEL	TG_hum_vit_Ctc_ctl_8h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	carbon tetrachloride_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016018013.CEL	TG_hum_vit_Ctc_ctl_8h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	carbon tetrachloride_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016018020.CEL	TG_hum_vit_Ctc_ctl_24h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	carbon tetrachloride_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016018021.CEL	TG_hum_vit_Ctc_ctl_24h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	carbon tetrachloride_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016018006.CEL	TG_hum_vit_Ctc_300um_2h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_2h	carbon tetrachloride_Low	Low	carbon tetrachloride	Steatotic_2h_Low	Steatotic_2h_Low			Steatotic_2h_Low		300.00	micromolar	2	hour
003016018007.CEL	TG_hum_vit_Ctc_300um_2h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_2h	carbon tetrachloride_Low	Low	carbon tetrachloride	Steatotic_2h_Low	Steatotic_2h_Low			Steatotic_2h_Low		300.00	micromolar	2	hour
003016018014.CEL	TG_hum_vit_Ctc_300um_8h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_8h	carbon tetrachloride_Low	Low	carbon tetrachloride	Steatotic_8h_Low	Steatotic_8h_Low			Steatotic_8h_Low		300.00	micromolar	8	hour
003016018015.CEL	TG_hum_vit_Ctc_300um_8h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_8h	carbon tetrachloride_Low	Low	carbon tetrachloride	Steatotic_8h_Low	Steatotic_8h_Low			Steatotic_8h_Low		300.00	micromolar	8	hour
003016018022.CEL	TG_hum_vit_Ctc_300um_24h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_24h	carbon tetrachloride_Low	Low	carbon tetrachloride	Steatotic_24h_Low	Steatotic_24h_Low			Steatotic_24h_Low		300.00	micromolar	24	hour
003016018023.CEL	TG_hum_vit_Ctc_300um_24h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_24h	carbon tetrachloride_Low	Low	carbon tetrachloride	Steatotic_24h_Low	Steatotic_24h_Low			Steatotic_24h_Low		300.00	micromolar	24	hour
003016018008.CEL	TG_hum_vit_Ctc_1500um_2h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_2h	carbon tetrachloride_Middle	Middle	carbon tetrachloride	Steatotic_2h_Middle		Steatotic_2h_Middle		Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	1500.00	micromolar	2	hour
003016018009.CEL	TG_hum_vit_Ctc_1500um_2h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_2h	carbon tetrachloride_Middle	Middle	carbon tetrachloride	Steatotic_2h_Middle		Steatotic_2h_Middle		Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	1500.00	micromolar	2	hour
003016018016.CEL	TG_hum_vit_Ctc_1500um_8h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	carbon tetrachloride_Middle	Middle	carbon tetrachloride	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	1500.00	micromolar	8	hour
003016018017.CEL	TG_hum_vit_Ctc_1500um_8h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	carbon tetrachloride_Middle	Middle	carbon tetrachloride	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	1500.00	micromolar	8	hour
003016018024.CEL	TG_hum_vit_Ctc_1500um_24h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	carbon tetrachloride_Middle	Middle	carbon tetrachloride	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	1500.00	micromolar	24	hour
003016018025.CEL	TG_hum_vit_Ctc_1500um_24h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	carbon tetrachloride_Middle	Middle	carbon tetrachloride	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	1500.00	micromolar	24	hour
003016018010.CEL	TG_hum_vit_Ctc_7500um_2h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_2h	carbon tetrachloride_High	High	carbon tetrachloride	Steatotic_2h_High			Steatotic_2h_High	Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	7500.00	micromolar	2	hour
003016018011.CEL	TG_hum_vit_Ctc_7500um_2h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_2h	carbon tetrachloride_High	High	carbon tetrachloride	Steatotic_2h_High			Steatotic_2h_High	Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	7500.00	micromolar	2	hour
003016018018.CEL	TG_hum_vit_Ctc_7500um_8h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	carbon tetrachloride_High	High	carbon tetrachloride	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	7500.00	micromolar	8	hour
003016018019.CEL	TG_hum_vit_Ctc_7500um_8h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	carbon tetrachloride_High	High	carbon tetrachloride	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	7500.00	micromolar	8	hour
003016018026.CEL	TG_hum_vit_Ctc_7500um_24h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	carbon tetrachloride_High	High	carbon tetrachloride	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	7500.00	micromolar	24	hour
003016018027.CEL	TG_hum_vit_Ctc_7500um_24h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	carbon tetrachloride_High	High	carbon tetrachloride	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	7500.00	micromolar	24	hour
003016075024.CEL	TG_hum_vit_Col_ctl_8h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_8h	colchicine_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016075025.CEL	TG_hum_vit_Col_ctl_8h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_8h	colchicine_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016075030.CEL	TG_hum_vit_Col_ctl_24h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_24h	colchicine_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016076030.CEL	TG_hum_vit_Col_ctl_24h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_24h	colchicine_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016075026.CEL	TG_hum_vit_Col_800um_8h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_8h	colchicine_Middle	Middle	colchicine	Non_steatotic_8h_Middle		Non_steatotic_8h_Control		Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	800.00	micromolar	8	hour
003016075027.CEL	TG_hum_vit_Col_800um_8h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_8h	colchicine_Middle	Middle	colchicine	Non_steatotic_8h_Middle		Non_steatotic_8h_Control		Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	800.00	micromolar	8	hour
003016076002.CEL	TG_hum_vit_Col_800um_24h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_24h	colchicine_Middle	Middle	colchicine	Non_steatotic_24h_Middle		Non_steatotic_24h_Control		Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	800.00	micromolar	24	hour
003016076003.CEL	TG_hum_vit_Col_800um_24h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_24h	colchicine_Middle	Middle	colchicine	Non_steatotic_24h_Middle		Non_steatotic_24h_Control		Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	800.00	micromolar	24	hour
003016075028.CEL	TG_hum_vit_Col_4000um_8h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_8h	colchicine_High	High	colchicine	Non_steatotic_8h_High			Non_steatotic_8h_Control	Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	4000.00	micromolar	8	hour
003016075029.CEL	TG_hum_vit_Col_4000um_8h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_8h	colchicine_High	High	colchicine	Non_steatotic_8h_High			Non_steatotic_8h_Control	Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	4000.00	micromolar	8	hour
003016076004.CEL	TG_hum_vit_Col_4000um_24h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_24h	colchicine_High	High	colchicine	Non_steatotic_24h_High			Non_steatotic_24h_Control	Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	4000.00	micromolar	24	hour
003016076005.CEL	TG_hum_vit_Col_4000um_24h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_24h	colchicine_High	High	colchicine	Non_steatotic_24h_High			Non_steatotic_24h_Control	Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	4000.00	micromolar	24	hour
003016065008.CEL	TG_hum_vit_Imi_ctl_8h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_8h	imipramine_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016065009.CEL	TG_hum_vit_Imi_ctl_8h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_8h	imipramine_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016065014.CEL	TG_hum_vit_Imi_ctl_24h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_24h	imipramine_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016065015.CEL	TG_hum_vit_Imi_ctl_24h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Control	none	Non_steatotic_24h	imipramine_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016065010.CEL	TG_hum_vit_Imi_3um_8h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_8h	imipramine_Middle	Middle	imipramine	Non_steatotic_8h_Middle		Non_steatotic_8h_Control		Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	3.00	micromolar	8	hour
003016065011.CEL	TG_hum_vit_Imi_3um_8h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_8h	imipramine_Middle	Middle	imipramine	Non_steatotic_8h_Middle		Non_steatotic_8h_Control		Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	3.00	micromolar	8	hour
003016065016.CEL	TG_hum_vit_Imi_3um_24h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_24h	imipramine_Middle	Middle	imipramine	Non_steatotic_24h_Middle		Non_steatotic_24h_Control		Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	3.00	micromolar	24	hour
003016065017.CEL	TG_hum_vit_Imi_3um_24h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_Middle	none	Non_steatotic_24h	imipramine_Middle	Middle	imipramine	Non_steatotic_24h_Middle		Non_steatotic_24h_Control		Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	3.00	micromolar	24	hour
003016065012.CEL	TG_hum_vit_Imi_15um_8h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_8h	imipramine_High	High	imipramine	Non_steatotic_8h_High			Non_steatotic_8h_Control	Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	15.00	micromolar	8	hour
003016065013.CEL	TG_hum_vit_Imi_15um_8h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_8h	imipramine_High	High	imipramine	Non_steatotic_8h_High			Non_steatotic_8h_Control	Non_steatotic_8h_MiddleHigh	Non_steatotic_8h_Control	15.00	micromolar	8	hour
003016065018.CEL	TG_hum_vit_Imi_15um_24h_1	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_24h	imipramine_High	High	imipramine	Non_steatotic_24h_High			Non_steatotic_24h_Control	Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	15.00	micromolar	24	hour
003016065019.CEL	TG_hum_vit_Imi_15um_24h_2	Non_Steatotic	Non_steatotic	Non_Steatotic_High	none	Non_steatotic_24h	imipramine_High	High	imipramine	Non_steatotic_24h_High			Non_steatotic_24h_Control	Non_steatotic_24h_MiddleHigh	Non_steatotic_24h_Control	15.00	micromolar	24	hour
003016060014.CEL	TG_hum_vit_Tam_ctl_8h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	tamoxifen_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016060015.CEL	TG_hum_vit_Tam_ctl_8h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	tamoxifen_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016060020.CEL	TG_hum_vit_Tam_ctl_24h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	tamoxifen_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016060021.CEL	TG_hum_vit_Tam_ctl_24h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	tamoxifen_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016060016.CEL	TG_hum_vit_Tam_5um_8h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	tamoxifen_Middle	Middle	tamoxifen	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	5.00	micromolar	8	hour
003016060017.CEL	TG_hum_vit_Tam_5um_8h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	tamoxifen_Middle	Middle	tamoxifen	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	5.00	micromolar	8	hour
003016060022.CEL	TG_hum_vit_Tam_5um_24h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	tamoxifen_Middle	Middle	tamoxifen	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	5.00	micromolar	24	hour
003016060023.CEL	TG_hum_vit_Tam_5um_24h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	tamoxifen_Middle	Middle	tamoxifen	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	5.00	micromolar	24	hour
003016060018.CEL	TG_hum_vit_Tam_25um_8h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	tamoxifen_High	High	tamoxifen	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	25.00	micromolar	8	hour
003016060019.CEL	TG_hum_vit_Tam_25um_8h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	tamoxifen_High	High	tamoxifen	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	25.00	micromolar	8	hour
003016060024.CEL	TG_hum_vit_Tam_25um_24h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	tamoxifen_High	High	tamoxifen	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	25.00	micromolar	24	hour
003016060025.CEL	TG_hum_vit_Tam_25um_24h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	tamoxifen_High	High	tamoxifen	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	25.00	micromolar	24	hour
003016037018.CEL	TG_hum_vit_Vpa_ctl_2h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_2h	valproic acid_Control	Control	none	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	NA		2	hour
003016037019.CEL	TG_hum_vit_Vpa_ctl_2h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_2h	valproic acid_Control	Control	none	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	Non_steatotic_2h_Control	NA		2	hour
003016037026.CEL	TG_hum_vit_Vpa_ctl_8h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	valproic acid_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016037027.CEL	TG_hum_vit_Vpa_ctl_8h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_8h	valproic acid_Control	Control	none	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	Non_steatotic_8h_Control	NA		8	hour
003016038004.CEL	TG_hum_vit_Vpa_ctl_24h_1	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	valproic acid_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016038005.CEL	TG_hum_vit_Vpa_ctl_24h_2	Steatotic	Non_steatotic	Steatotic_Control	none	Non_steatotic_24h	valproic acid_Control	Control	none	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	Non_steatotic_24h_Control	NA		24	hour
003016037020.CEL	TG_hum_vit_Vpa_200um_2h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_2h	valproic acid_Low	Low	valproic acid	Steatotic_2h_Low	Steatotic_2h_Low			Steatotic_2h_Low		200.00	micromolar	2	hour
003016037021.CEL	TG_hum_vit_Vpa_200um_2h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_2h	valproic acid_Low	Low	valproic acid	Steatotic_2h_Low	Steatotic_2h_Low			Steatotic_2h_Low		200.00	micromolar	2	hour
003016037028.CEL	TG_hum_vit_Vpa_200um_8h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_8h	valproic acid_Low	Low	valproic acid	Steatotic_8h_Low	Steatotic_8h_Low			Steatotic_8h_Low		200.00	micromolar	8	hour
003016037029.CEL	TG_hum_vit_Vpa_200um_8h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_8h	valproic acid_Low	Low	valproic acid	Steatotic_8h_Low	Steatotic_8h_Low			Steatotic_8h_Low		200.00	micromolar	8	hour
003016038006.CEL	TG_hum_vit_Vpa_200um_24h_1	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_24h	valproic acid_Low	Low	valproic acid	Steatotic_24h_Low	Steatotic_24h_Low			Steatotic_24h_Low		200.00	micromolar	24	hour
003016038007.CEL	TG_hum_vit_Vpa_200um_24h_2	Steatotic	Steatotic	Steatotic_Low	low	Steatotic_24h	valproic acid_Low	Low	valproic acid	Steatotic_24h_Low	Steatotic_24h_Low			Steatotic_24h_Low		200.00	micromolar	24	hour
003016037022.CEL	TG_hum_vit_Vpa_1000um_2h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_2h	valproic acid_Middle	Middle	valproic acid	Steatotic_2h_Middle		Steatotic_2h_Middle		Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	1000.00	micromolar	2	hour
003016037023.CEL	TG_hum_vit_Vpa_1000um_2h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_2h	valproic acid_Middle	Middle	valproic acid	Steatotic_2h_Middle		Steatotic_2h_Middle		Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	1000.00	micromolar	2	hour
003016037030.CEL	TG_hum_vit_Vpa_1000um_8h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	valproic acid_Middle	Middle	valproic acid	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	1000.00	micromolar	8	hour
003016038001.CEL	TG_hum_vit_Vpa_1000um_8h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_8h	valproic acid_Middle	Middle	valproic acid	Steatotic_8h_Middle		Steatotic_8h_Middle		Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	1000.00	micromolar	8	hour
003016038008.CEL	TG_hum_vit_Vpa_1000um_24h_1	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	valproic acid_Middle	Middle	valproic acid	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	1000.00	micromolar	24	hour
003016038009.CEL	TG_hum_vit_Vpa_1000um_24h_2	Steatotic	Steatotic	Steatotic_Middle	middle	Steatotic_24h	valproic acid_Middle	Middle	valproic acid	Steatotic_24h_Middle		Steatotic_24h_Middle		Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	1000.00	micromolar	24	hour
003016037024.CEL	TG_hum_vit_Vpa_5000um_2h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_2h	valproic acid_High	High	valproic acid	Steatotic_2h_High			Steatotic_2h_High	Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	5000.00	micromolar	2	hour
003016037025.CEL	TG_hum_vit_Vpa_5000um_2h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_2h	valproic acid_High	High	valproic acid	Steatotic_2h_High			Steatotic_2h_High	Steatotic_2h_MiddleHigh	Steatotic_2h_MiddleHigh	5000.00	micromolar	2	hour
003016038002.CEL	TG_hum_vit_Vpa_5000um_8h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	valproic acid_High	High	valproic acid	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	5000.00	micromolar	8	hour
003016038003.CEL	TG_hum_vit_Vpa_5000um_8h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_8h	valproic acid_High	High	valproic acid	Steatotic_8h_High			Steatotic_8h_High	Steatotic_8h_MiddleHigh	Steatotic_8h_MiddleHigh	5000.00	micromolar	8	hour
003016038010.CEL	TG_hum_vit_Vpa_5000um_24h_1	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	valproic acid_High	High	valproic acid	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	5000.00	micromolar	24	hour
003016038011.CEL	TG_hum_vit_Vpa_5000um_24h_2	Steatotic	Steatotic	Steatotic_High	high	Steatotic_24h	valproic acid_High	High	valproic acid	Steatotic_24h_High			Steatotic_24h_High	Steatotic_24h_MiddleHigh	Steatotic_24h_MiddleHigh	5000.00	micromolar	24	hour

# Set input parameters         
cutOffAdj.P.Val <- 0.05
cutOfflogFC <- 0
cutOffAveExpr <- 6
cutOffPval <- 0.05 #used if Adj.P.Val removes all

# Groups to compare
Description_column<-"Group"
InterestGroup<- "Steatotic"
Controls<-"Non_steatotic"

Subset input tables. Only include data relevant to current analysis

# remove unused metadata
descriptionTable2<-descriptionTable[,c("Array", "Name", Description_column)]
write.table(descriptionTable2, paste0(descriptionFile, "_sub.txt"), row.names=FALSE, quote=FALSE, sep="\t")

# remove unused samples
descriptionTable2<- descriptionTable2[c(grep(InterestGroup,descriptionTable2[,Description_column]), grep(Controls,descriptionTable2[,Description_column])),]
colnames(descriptionTable2)<-c("Array", "Name", "experimentFactor")
normDataTable<-normDataTable[,c(descriptionTable2$Name)]

Amount of samples per group
Var1	Freq
Non_steatotic	46
Steatotic	62

PCA plot to exclude the post-processing outliers replicates

Creating UMAP plots

Data structuring & cleaning

Statistical analysis with limma

## --[[ Saving table for contrast Steatoticx1+Non_steatoticx-1 ]]--

Displaying top 6 genes, to check data & pipeline correctness

Plotting histograms

## [1] "p-value histograms"
## --[[ Saving Steatoticx1+Non_steatoticx-1.txt P.Value_hist.png ]]--

## [1] "adapted fold change histograms"
## --[[ Saving Steatoticx1+Non_steatoticx-1.txt FC_hist.png ]]--

Creating table based on the cut-offs

## [1] "Creating table based on the cut-offs"
## [1] "Applying cutOffAveExpr (6) removed 11642 genes. 8272 genes remain."
## [1] "Additionally, applying cutOfflogFC (0) removed 0 genes. 8272 genes remain."
## [1] "Additionally, applying cutOffAdj.P.Val (0.05) removed 5125 genes. 3147 genes remain."
## --[[ Saving table Steatoticx1+Non_steatoticx-1_chosen_cutOff.txt ]]--

Creating UMAP based on DEGs

Creating UMAP plots

List of differentially expressed genes (DEGs)

## R version 4.3.1 (2023-06-16 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=Dutch_Netherlands.utf8  LC_CTYPE=Dutch_Netherlands.utf8   
## [3] LC_MONETARY=Dutch_Netherlands.utf8 LC_NUMERIC=C                      
## [5] LC_TIME=Dutch_Netherlands.utf8    
## 
## time zone: Europe/Amsterdam
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] gdata_3.0.0   limma_3.56.2  umap_0.2.10.0 plotly_4.10.3 ggplot2_3.4.4
## [6] DT_0.30       knitr_1.45   
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.7        utf8_1.2.4        generics_0.1.3    tidyr_1.3.0      
##  [5] gtools_3.9.4      lattice_0.21-8    digest_0.6.33     magrittr_2.0.3   
##  [9] evaluate_0.23     grid_4.3.1        fastmap_1.1.1     jsonlite_1.8.7   
## [13] Matrix_1.5-4.1    RSpectra_0.16-1   httr_1.4.7        purrr_1.0.2      
## [17] fansi_1.0.5       crosstalk_1.2.0   viridisLite_0.4.2 scales_1.2.1     
## [21] lazyeval_0.2.2    jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1      
## [25] ellipsis_0.3.2    munsell_0.5.0     yaml_2.3.7        withr_2.5.2      
## [29] cachem_1.0.8      tools_4.3.1       dplyr_1.1.3       colorspace_2.1-0 
## [33] reticulate_1.34.0 vctrs_0.6.4       R6_2.5.1          png_0.1-8        
## [37] lifecycle_1.0.4   htmlwidgets_1.6.2 pkgconfig_2.0.3   pillar_1.9.0     
## [41] bslib_0.5.1       gtable_0.3.4      data.table_1.14.8 glue_1.6.2       
## [45] Rcpp_1.0.11       xfun_0.39         tibble_3.2.1      tidyselect_1.2.0 
## [49] highr_0.10        farver_2.1.1      htmltools_0.5.5   rmarkdown_2.25   
## [53] compiler_4.3.1    askpass_1.2.0     openssl_2.1.1

End of Report